147 lines
6.2 KiB
Groff
147 lines
6.2 KiB
Groff
LAMMPS (11 Aug 2017)
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### Pure diffusion with a reaction source term analog of a periodic ###
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### Poiseuille flow problem using transport DPD (tDPD) simulation ###
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### ###
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### Created : Zhen Li (zhen_li@brown.edu) ###
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### Division of Applied Mathematics, Brown University. ###
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### ###
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### tDPD system setup follows Fig.1 in the publication: ###
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### Z. Li, A. Yazdani, A. Tartakovsky and G.E. Karniadakis. ###
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### "Transport dissipative particle dynamics model for mesoscopic ###
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### advection-diffusion-reaction problems. J. Chem. Phys., ###
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### 2015, 143: 014101. DOI: 10.1063/1.4923254 ###
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########################################################################
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units lj
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dimension 3
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boundary p p p
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neighbor 0.2 bin
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neigh_modify every 1 delay 0 check yes
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atom_style tdpd 2
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region tdpd block -10 10 -10 10 -5 5 units box
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create_box 1 tdpd
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Created orthogonal box = (-10 -10 -5) to (10 10 5)
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1 by 1 by 1 MPI processor grid
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create_atoms 1 random 16000 276438 NULL
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Created 16000 atoms
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mass 1 1.0
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set atom * cc 1 1.0
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16000 settings made for cc index 1
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set atom * cc 2 1.0
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16000 settings made for cc index 2
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pair_style tdpd 1.0 1.58 9872598
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pair_coeff 1 1 18.75 4.5 0.41 1.58 1.58 1.0 1.0E-5 2.0 3.0 1.0E-5 2.0
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compute mythermo all temp
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thermo 50
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thermo_modify temp mythermo
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thermo_modify flush yes
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velocity all create 1.0 432982 loop local dist gaussian
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fix mvv all mvv/tdpd 0.5
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fix upper1 all tdpd/source 1 cuboid 0.0 5.0 0.0 20.0 10.0 10.0 0.01
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fix lower1 all tdpd/source 1 cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 -0.01
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fix upper2 all tdpd/source 2 cuboid 0.0 5.0 0.0 20.0 10.0 10.0 -0.01
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fix lower2 all tdpd/source 2 cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 0.01
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timestep 0.01
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run 500
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Neighbor list info ...
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 1.78
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ghost atom cutoff = 1.78
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binsize = 0.89, bins = 23 23 12
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair tdpd, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 11.3 | 11.3 | 11.3 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 1 48.948932 0 50.448838 202.19166
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50 0.99837766 43.949877 0 45.447349 195.80936
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100 0.99846831 43.756995 0 45.254604 198.22348
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150 1.0026903 43.72408 0 45.228021 196.61676
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200 1.0063144 43.722388 0 45.231765 194.17954
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250 1.0032304 43.721864 0 45.226615 197.85829
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300 0.9932656 43.703526 0 45.193331 196.57406
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350 1.0002916 43.720498 0 45.220841 193.55346
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400 0.99475486 43.722965 0 45.215004 196.81546
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450 1.0011803 43.712447 0 45.214124 200.46118
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500 1.0009006 43.708984 0 45.210241 197.38953
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Loop time of 96.0326 on 1 procs for 500 steps with 16000 atoms
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Performance: 4498.474 tau/day, 5.207 timesteps/s
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99.9% CPU use with 1 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 90.083 | 90.083 | 90.083 | 0.0 | 93.80
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Neigh | 5.049 | 5.049 | 5.049 | 0.0 | 5.26
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Comm | 0.34141 | 0.34141 | 0.34141 | 0.0 | 0.36
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Output | 0.00092816 | 0.00092816 | 0.00092816 | 0.0 | 0.00
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Modify | 0.45991 | 0.45991 | 0.45991 | 0.0 | 0.48
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Other | | 0.09865 | | | 0.10
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Nlocal: 16000 ave 16000 max 16000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 14091 ave 14091 max 14091 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 749379 ave 749379 max 749379 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 749379
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Ave neighs/atom = 46.8362
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Neighbor list builds = 183
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Dangerous builds = 0
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reset_timestep 0
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compute cc1 all tdpd/cc/atom 1
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compute cc2 all tdpd/cc/atom 2
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compute bin all chunk/atom bin/1d y 0.0 1.0
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fix stat all ave/chunk 1 100 100 bin c_cc1 c_cc2 norm sample file cc.profile
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run 100
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Per MPI rank memory allocation (min/avg/max) = 11.8 | 11.8 | 11.8 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 1.0009006 43.708984 0 45.210241 199.3205
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50 1.0007276 43.704844 0 45.205842 197.77053
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100 1.0039032 43.714201 0 45.219961 197.31118
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Loop time of 19.0326 on 1 procs for 100 steps with 16000 atoms
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Performance: 4539.577 tau/day, 5.254 timesteps/s
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99.9% CPU use with 1 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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Pair | 17.842 | 17.842 | 17.842 | 0.0 | 93.74
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Neigh | 0.98674 | 0.98674 | 0.98674 | 0.0 | 5.18
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Comm | 0.066013 | 0.066013 | 0.066013 | 0.0 | 0.35
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Output | 0.00016284 | 0.00016284 | 0.00016284 | 0.0 | 0.00
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Modify | 0.11795 | 0.11795 | 0.11795 | 0.0 | 0.62
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Other | | 0.02012 | | | 0.11
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Nlocal: 16000 ave 16000 max 16000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 14126 ave 14126 max 14126 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 748927 ave 748927 max 748927 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 748927
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Ave neighs/atom = 46.8079
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Neighbor list builds = 37
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Dangerous builds = 0
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Please see the log.cite file for references relevant to this simulation
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Total wall time: 0:01:55
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